Changes between Version 63 and Version 64 of NTTData

Timestamp:

Nov 4, 2021, 2:07:32 PM (4 years ago)

Author:

Elaine Meng

Comment:

--

NTTData

@@ -401 +401 @@
 Some discussion of !AlphaFold vs. !RosettaFold.  Yifan Cheng tried connecting proteins with a linker and using !AlphaFold but that did not predict the dimer correctly.
 
-== 10/21/2021 ==
+== 11/4/2021 ==
 
 Phil, Philip, Darrell; Scooter, Elaine, Eric, TomG, Zach, Greg
@@ -409 +409 @@
 Scooter: need to start thinking about the next year's contract soon. Let's start brainstorming in some meeting(s) soon, including what we did and didn't do from the previous contracts. Darrell: sounds good. Don't worry too much about the specifics, since plans have to evolve when other projects (E.g. hubmap) don't progress as expected.
 
-Phil: By the way, I've seen others using ChimeraX recently, including for getting alphafold models. Are there any ongoing issues with the pipeline?  Philip: not much, they have been resolved with fixes in daily build. Still have problems with FTP of EMDB maps.  TomG: FTP is much better for general user populace (more reliable and faster), but I can add an option to use HTTPS instead. Discussion of whether recent changes for pipeline can go into 1.3 release or not... Eric will have to check on that. 
+Phil: By the way, I've seen others using ChimeraX recently, including for getting alphafold models. Are there any ongoing issues with the pipeline?  Philip: not much, they have been resolved with fixes in daily build. Still have problems with FTP of EMDB maps.  TomG: FTP is much better for general user populace (more reliable and faster), but I can add an option to use HTTPS instead, as long as you can tolerate extreme slowness in some cases. Will get it in next week. Discussion of whether recent changes for pipeline can go into 1.3 release or not... Eric will have to check on that. 
+
+Eric: Phil, did you and Darrell discuss the coloring of structures with >6 chains?  Darrell: yes, but... may depend on situation, what you are trying to show.  Phil: lean against "rainbow" [...] much discussion of coloring symmetry copies the same vs. color by entity (sequence) vs. color by polymer type vs. cycling through some standard palette of 6 colors.  Darrell: we can provide more alternatives for a given structure and allow users to choose which one(s) they want. Elaine: color by symmetry copies would require some new code. Darrell: we should ask our medical illustrator for advice on an expanded palette.  Scooter, Elaine: try colorbrewer.org  Elaine: these are already in ChimeraX palettes (names can be used with the "palette" option of "color"), as an added bonus.